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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataaatttttgccattgctttgagaatctttgtccctgcgctgcccccaaacagtacataagtctgatcaaaagcaagaaaaatagttataaat...

Basic information

species Vitis vinifera
transcript Vv13s0019g03960.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA20G31830.1 (Glycine max), 5'ss of exon 7
GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataaatttttgccattgctttgaga-atctttgtccctgcgctgcccccaaacagtacataagtctgatcaaaagcaagaaaaatagttataaat
|| ||||||||||| |||||| | ||||| |||| ||| ||  | ||| | ||| ||||||| ||||||||||||||||||  ||||   | ||| |     | |  || ||  |   |  || ||       | ||  | ||  | |    |   |     | ||  | || | || |
GAAGAATGCAAACGTGTATCAACTGAGGGGCAAAACTTAAGGCTGGACTTGTCAGCCAAGTTTCAAGATGCAATCAAGgttggaatattgtcttgtctagaatgtatgatattctgaccagtgtgcattgggtatact-tgcactatttaatttctattggtggaatgtggtcaaaagt
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351029666|gb|FQ427506.1|FQ427506
EST:     GCCAAACCTTGAAATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG                         GACGTAAGCGGTAAGCTTGGAA
genomic: GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCT-GGAA
EST: gi|110726208|gb|EE101788.1|EE101788
EST:     AGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG                         GACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
genomic: AGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
EST: gi|110711711|gb|EE088504.1|EE088504
EST:     CCAAACCTTTGAGAT-AGACCTATCANCCAAGTTCCNAGATGCAATCAAG                         GACGTAAGCAGTAAGCTGGAAG-GCAAAAA
genomic: CCAAACCTT-GAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAA
EST: gi|30255027|gb|CB971474.1|CB971474
EST:     GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG                         GACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
genomic: GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
EST: gi|110713047|gb|EE088636.1|EE088636
EST:     CCAA-CCTTGAGATTAGACCTATCAACCAAGT-CCNAGAATGCA-TCAAG                         GACGTAAGCAGTAAGCTGGAAGAGCAAAAAGA
genomic: CCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGA-TGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAAGA
EST: gi|30254970|gb|CB971417.1|CB971417
EST:     GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG                         GACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
genomic: GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
EST: gi|110721939|gb|EE097735.1|EE097735
EST:     GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAAATGCAATCAAG                         GACTTAAGCAGT
genomic: GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGT
EST: gi|110727231|gb|EE103758.1|EE103758
EST:     GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAG                         GACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
genomic: GCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGAGCAAAAAGACGAGTGTCTCTCCCAGCTC
EST: gi|110711601|gb|EE088266.1|EE088266
EST:     CCCAACCTTGAGAATAGACCTATCAACCAAGTTCCCAGAATGCA-TCAAG                         GACGTAAGCAGTAAGCTGGAAGAAGCAAAA
genomic: CCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGA-TGCAATCAAGgttttaataa ... cttgttatagGACGTAAGCAGTAAGCTGGAAGA-GCAAAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAATGCAAACGAGTATCAGCAGAGGGCCAAACCTTGAGATTAGACCTATCAACCAAGTTCCAAGATGCAATCAAGgttttaataaatttttgccattgctttgagaatctttgtccctgcgctgcccccaaacagtacataagtctgatcaaaagcaagaaaaatagttataaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa